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Platform GPL5856 Query DataSets for GPL5856
Status Public on Dec 13, 2007
Title JCVI PFGRC Listeria monocytogenes 21K v3 array designed primarily based on strain EGD-e
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Listeria monocytogenes
Manufacturer JCVI PFGRC
Manufacture protocol 3QLM, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000
Support glass
Coating aminosilane
 
Description This set includes 6322 oligonucleotides, has 21168 spots distributed in 48 blocks.
 
Web link http://pfgrc.jcvi.org/descriptionPages.shtml
Submission date Sep 13, 2007
Last update date Mar 17, 2010
Contact name PFGRC JCVI
E-mail(s) jli@jcvi.org
Phone 3017957840
Organization name J. Craig Venter Institute
Department PFGRC
Street address 9704 Medical Center Drive
City Rockville
State/province MD
ZIP/Postal code 20850
Country USA
 
Samples (32) GSM619069, GSM619070, GSM619071, GSM619072, GSM619073, GSM619074 
Series (1)
GSE25195 Transcriptional response of Listeria monocytogenes h7858 and f6854 to lactate and acetate

Data table header descriptions
ID
SEQUENCE Oligo sequence
GC% GC content of the sequence
Internal Repeat Score Internal repeat score
Self-Annealing Score Self-anneal score
Primary Strain The strain of primary target
Primary Target Locus primarily hit by the oligo
Common Name of Primary Target Common name of primary target
Gene Symbol Gene symbol
Strain 1/2a F6854 Target map of strain 1/2a F6854
Strain 4b F2365 Target map of strain 4b F2365
Strain 4b H7858 Target map of strain 4b H7858
Strain EGD-e Target map of strain EGD-e
ORF primary target link in Entrez Gene
SPOT_ID

Data table
ID SEQUENCE GC% Internal Repeat Score Self-Annealing Score Primary Strain Primary Target Common Name of Primary Target Gene Symbol Strain 1/2a F6854 Strain 4b F2365 Strain 4b H7858 Strain EGD-e ORF SPOT_ID
3QLM00001_A_1 AAAAGATGTTGGTATCGATTTAGGTACAGCCAATGTATTAATTCATGTTAAAGGAAGAGGAATCGTCGTT 34.29 31 118 EGD-e lmo2525 similar to MreB-like protein mbl LMOf6854_2587::70::100.0::3.9E-11::+ LMOf2365_2498::70::100.0::3.9E-11::+ LMOh7858_2677::70::100.0::3.9E-11::+ lmo2525::70::100.0::3.9E-11::+ lmo2525
3QLM00001_A_10 GGGGGTAGTGAAAATGGGAAATAAAAAAGTGAAGCGAAAACTTGGCGCTAATATTTGGTGGATACTTATA 37.14 32 65 4b F2365 LMOf2365_0703 hypothetical protein LMOf2365_0703::70::100.0::5.0E-11::+ LMOh7858_0731.1::57::100.0::4.9E-8::+ LMOf2365_0703
3QLM00001_A_11 AAAAATCTTGGTATATTTATAAACGTTGCTGATGCGGACAAAACGCTTTCGCAACAAAAGAAACTGACCT 35.71 31 93 4b F2365 LMOf2365_2562 hypothetical protein LMOf6854_2425.1::70::98.57143::1.8E-10::+ LMOf2365_2562::70::100.0::7.1E-11::+,LMOf2365_2336::70::98.57143::1.8E-10::+ LMOh7858_2507.1::70::98.57143::1.8E-10::+ LMOf2365_2562
3QLM00001_A_12 CAATTCAAGTGAAAATAGGCGTAAAAAAACAGGATTTCCTCCATAAAATAGGAAGTAATCCTGTTTCTTA 31.43 31 132 1/2a F6854 LMOf6854_1510.1 hypothetical protein LMOf6854_1510.1::70::100.0::5.0E-11::+ LMOh7858_1563.1::70::94.28571::2.1E-9::+ LMOf6854_1510.1
3QLM00001_A_13 GGTTTTCCGTTGTTGTTTTATTCAGAAAATATAGTAAAAAATGTTTCACGTGAAACATTTGAAAAAGCCG 30.0 33 127 4b F2365 LMOf2365_2747 hypothetical protein LMOf2365_2747::70::100.0::7.1E-11::+ LMOf2365_2747
3QLM00001_A_14 GATTCGTACTCTTGTCTACGCAGTTGGCTCCAAAAACGATAAGAAGATTCGTCTTGAAATTATCGAATAA 37.14 29 102 EGD-e lmo1796 similar to unknown protein LMOf6854_1854.1::70::100.0::5.0E-11::+ LMOf2365_1823::70::98.57143::7.3E-11::+ LMOh7858_1921.1::70::98.57143::7.3E-11::+ lmo1796::70::100.0::2.9E-11::+ lmo1796
3QLM00001_A_15 CATTTCTAATAAACAAATGATATTATTAACACACATAGGAGATGAAAAAATCGCCTATAAGCAACATACC 28.57 30 82 1/2a F6854 LMOf6854_1307.1 conserved hypothetical protein LMOf6854_1307.1::70::100.0::7.1E-11::+ LMOf2365_1285::70::100.0::7.1E-11::+ LMOf6854_1307.1
3QLM00001_A_16 TCCATAAAAAATATAGAAAAGAGATGGAATTTGATCCGAAAATCAATCAAGACGGAATAAAACTGTTCCA 30.0 31 89 4b H7858 LMOh7858_0080.4 hypothetical protein LMOh7858_0080.4::70::100.0::5.0E-11::+ LMOh7858_0080.4
3QLM00001_A_17 AAAAGTGGGAAGTATTCGCAGTTCAAAACGTCGAGGCAGCAGAGGAAATCATCAACAAATTAGTAAGTGA 40.0 31 53 EGD-e lmo1643 unknown LMOf6854_1698.2::70::100.0::7.1E-11::+ LMOf2365_1664::70::95.71428::2.6E-10::+ LMOh7858_1758.1::70::94.28571::6.6E-10::+ lmo1643::70::100.0::1.6E-11::+ lmo1643
3QLM00001_A_18 AAATATGCATTCACTGAAACATTGATAGATGTTAGTCTTTTAGATGTGAGAGTAGAACAAGTTTTAATGA 28.57 31 95 4b H7858 LMOh7858_0479.7 hypothetical protein LMOh7858_0479.7::70::100.0::5.0E-11::+ LMOh7858_0479.7
3QLM00001_A_19 TGCTTATTTTATCTTTAGAAGACTTTAGCCAAATTGAATCTGCCTCTACTGCCTTGGATCAAAATGCCGG 38.57 32 112 1/2a F6854 LMOf6854_1756 methyl-accepting chemotaxis protein LMOf6854_1756::70::100.0::3.3E-11::+ LMOf2365_1723::70::100.0::3.3E-11::+ LMOh7858_1823::70::100.0::3.3E-11::+ lmo1699::70::97.14286::2.3E-10::+ LMOf6854_1756
3QLM00001_A_2 TTAGTCCATACTATTTTATCCATAAAGAAGCATTTGTGCAACTGTTTGGTTTGAATATTTTTTTAATTTG 25.71 32 87 4b F2365 LMOf2365_2001 hypothetical protein LMOf2365_2001::70::100.0::5.2E-11::+ LMOf2365_2001
3QLM00001_A_20 CTTGGTTAATATATAGTCATAAGCTAACAACAAGCAAAACATTTTCATTCTTCTCCCCCCTTTTAGAATG 32.86 30 82 4b F2365 LMOf2365_0235 hypothetical protein LMOf6854_0232.2::70::98.57143::9.3E-11::+,LMOf6854_0232.1::70::95.71428::1.6E-9::+ LMOf2365_0235::70::100.0::4.9E-11::+,LMOf2365_0236::70::98.591545::1.3E-10::+ LMOh7858_0247::70::98.591545::1.6E-10::+,LMOh7858_0247::70::98.591545::1.6E-10::+,LMOh7858_0243.1::70::95.71428::1.1E-9::+,LMOh7858_0243.1::70::95.71428::2.1E-9::+,LMOh7858_0246::70::95.71428::3.4E-9::+ LMOf2365_0235
3QLM00001_A_21 TGAAGTCAGATTTAGGGGAGCTACACCCGGATAACGTGGCTAAAAGCAATACAAAGATGGTCGCAGCCAT 47.14 28 71 Obsolete Obsolete Obsolete LMOf2365_2387::70::100.0::4.3E-11::- LMOh7858_2563::70::100.0::4.3E-11::- lmo2416::70::100.0::4.3E-11::- --obsolete
3QLM00001_A_22 AATGAAAAAAGATATAATTCTCAAATCAGTTGTTATATCAATCATTACAGCCATAGTTTTCAACATTAAG 24.29 31 121 4b F2365 LMOf2365_2539 hypothetical protein LMOf2365_2539::70::100.0::4.9E-11::+ LMOf2365_2539
3QLM00001_A_23 TTTTTTGCGTAATCAAAAAGCGCTTACAAAAGAGGAGGAGAAATATTGCATAAAACAGCCAGAAAAATGG 34.29 31 85 1/2a F6854 LMOf6854_2629.1 hypothetical protein LMOf6854_2629.1::70::100.0::7.1E-11::+ LMOf6854_2629.1
3QLM00001_A_24 TTTCAGCTCAGAAACTTATACCATTGATATGAAACACGAACCCAAAGCACCAAAATCTATTTACCAATTA 32.86 31 68 4b F2365 LMOf2365_2750 hypothetical protein LMOf2365_2750::70::100.0::4.9E-11::+ LMOh7858_3026.1::70::100.0::2.1E-11::+ LMOf2365_2750
3QLM00001_A_3 CACTTTGGAAGTGGAAATTGGTTTAGGCGAATTAAATAGATTTTTACTTCATAAGTCTAAACAAAATTAA 27.14 31 128 4b F2365 LMOf2365_0323 hypothetical protein LMOf2365_0323::70::100.0::7.6E-11::+ LMOf2365_0323
3QLM00001_A_4 TCAGACAGTTTAATAAAAGCGATGATTAATTTTATTTTATTGATTGAGGCTTATTCTTTGCTCTTAGTAG 27.14 31 96 1/2a F6854 LMOf6854_0096.1 hypothetical protein LMOf6854_0096.1::70::100.0::5.2E-11::+ LMOf6854_0096.1
3QLM00001_A_5 CTGGGATTTTAATAATCCTGAGTCAATGAAAGCATGGGATTTGGCTTCTGGTTCTTATGCAGAACAAGTT 38.57 30 77 EGD-e lmo0145 hypothetical protein LMOf2365_0161::70::100.0::2.8E-11::+ LMOh7858_0162.8::70::100.0::2.8E-11::+ lmo0145::70::100.0::7.6E-11::+ lmo0145

Total number of rows: 6827

Table truncated, full table size 1656 Kbytes.




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